Development of a device to trap soil bacteria capable of degrading organic contaminants such as alkanes and polycyclic aromatic hydrocarbons

Abstract

The microbial biodegradation potential of contaminated sites is critical for efficient bioremediation, particularly through bioaugmentation with microorganisms that degrade organic pollutants. The BactoTrapS tool was developed to select and enrich bacteria tolerant to contaminants and capable of biodegradation directly from soils. It comprises a nylon mesh filled with activated carbon or vermiculite spiked with PAHs (phenanthrene, pyrene, dibenzo-a,h-anthracene) or alkanes (n-hexadecane, cyclohexane), while control traps remained unspiked. After five weeks of soil incubation, spiked traps showed significantly higher mineralisation. Bacterial colonisation was evaluated via CFU counts and 16S rDNA qPCR, revealing increased densities in spiked conditions. Alpha diversity analysis showed reduced diversity in spiked traps, while beta diversity confirmed selective enrichment of genera such as Mycobacterium and Polaromonas under PAHs, and Nocardioides and Nocardia under alkanes. These genera were identified as indicator species for the respective contaminants. qPCR of key biodegradation genes (PAH-RHDα, AlkB, CYP153) revealed elevated gene copy numbers in spiked traps. Most isolates from spiked conditions metabolised phenanthrene and hexadecane as sole carbon sources. BactoTrapS offers a rapid, efficient method to enrich biodegrading bacteria for hydrocarbons and other organic contaminants, promising broad applicability for future remediation efforts.

Keywords: Alkane; Bacteria; BactoTrapS; Isolates; Metabarcoding; PAH; Soil.